Hi Dapeng, We run RepeatMasker using consensus sequence library files provided by RepBase Update at http://girinst.org/ . It's possible that the particular LTRs mentioned in the paper are not yet in the library, or at least were not at the time we ran RepeatMasker.
The authors of RepeatMasker know much more about the state of the libraries, and repetitive sequences in general -- I suggest you contact them, see http://repeatmasker.org/ . Hope that helps, and if you have any more questions about the UCSC Genome Browser, please email us at [email protected]. Angie ----- Original Message ----- > From: "wangdp" <[email protected]> > To: "genome" <[email protected]> > Sent: Wednesday, February 8, 2012 7:02:32 PM > Subject: [Genome] A question about the absence of LTR in anole genome > usingrepeatmasker results > Dear Sir, > I am using the repeatmasker result from the UCSC data in anole genome > (version2.0). > But I found no LTR repeat results in this table. > In contrast, One paper has indicated the existence of LTR in anole > genome. Please refer to the reference "The evolution of two partner > LINE/SINE families and a full-length chromodomain-containing Ty3/Gypsy > LTR element in the first reptilian genome of Anolis carolinensis" . > _____________________________________________________________________ > "LTR retroelements (LTR retrotransposons and retroviruses) repre-sent > the second sub-type of class I TEs. The genome of Anolis harbours > a number of previously characterized LTR retrotransposons, which > represent less than 0.2% of the total genomic sequence ( Table 2 ). > Furthermore, we identified N 20,0 0 0 copies of a new LTR > retro-transposon which account for approximately 2% of the genomic > sequence of Anolis ( Table 2 ). These copies pertain to a novel > element > belonging to the Ty3/Gypsy ( Metaviridae) group, which spreads in a > wide number of plant, fungi and animal genomes (for more details see > Eickbush and Malik 20 02)." > _____________________________________________________________________ > Could you please help me about this? > Many thanks for your help, > Best wishes, > Sincerely, > Dapeng > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
